<PAGE>   1

                      SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, DC 20549
                                 FORM 10-K/A

                              AMENDMENT NO. 1 TO

(Mark One)
    X            ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d)
   ----             OF THE SECURITIES EXCHANGE ACT OF 1934

                    For the fiscal year ended March 31, 1999

                                       OR

                TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
  ----               OF THE SECURITIES EXCHANGE ACT OF 1934
                       For the transition period from ___ to ___

                          Commission file number 0-6355

                             GROUP 1 SOFTWARE, INC.
             (Exact name of registrant as specified in its charter)

<TABLE>
<CAPTION>
<S>                                           <C>
             DELAWARE                                    52-0852578
  (State or other jurisdiction                (IRS Employer Identification No.)
  of incorporation or organization)

4200 Parliament Place, Suite 600, Lanham, MD             20706-1860
 (Address of principal executive offices)                (ZIP Code)
</TABLE>

       Registrant's telephone number, including area code: (301) 918-0400

Securities registered pursuant to Section 12(b) of the Act: NONE
Securities registered pursuant to Section 12(g) of the Act: Common Stock $0.50
                                                            par value

Indicate by check mark whether the Registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the Registrant was
required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.

                                  YES X  NO
                                     ---   ----

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of the Registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. ( )

The aggregate market value of the voting stock held by non-affiliates of the
Registrant on June 23, 1999 was $32,596,288.

The number of shares of the Registrant's Common Stock outstanding on June 23,
1999 was 3,725,290.

                      DOCUMENTS INCORPORATED BY REFERENCE:

Definitive proxy statement to be filed with the Securities and Exchange
Commission relating to Company's 1999 Annual Meeting of Shareholders (Part III
of Form 10-K).


                                        1
<PAGE>   2



                                     PART IV

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND

         REPORTS ON FORM 10-K

<TABLE>
<CAPTION>


<S>      <C>
         1.   Financial Statements:

              The following financial statements are submitted in Item 8:

                      Report of Independent Accountants on  Financial Statements

                      Consolidated Balance Sheets as of March 31, 1999 and 1998

                      Consolidated Statements of Operations for the  years
                      ended March 31, 1999, 1998 and 1997

                      Consolidated Statements of Comprehensive Income for the
                      years ended March 31, 1999, 1998 and 1997

                      Consolidated Statements of Stockholders' Equity  for the years
                      ended March 31, 1999, 1998 and 1997

                      Consolidated Statements of Cash Flows for the  years
                      ended March 31, 1999, 1998 and 1997

                      Notes to Consolidated Financial Statements for  the years
                      ended March 31, 1999, 1998 and 1997

         2.   Financial Statement Schedules

              The following financial statement schedule is filed as part of this report:

                       Report of Independent Accountants on Financial Statement
                       Schedule

                       Schedule II: Valuation and Qualifying Accounts for the Years
                       Ended March 31, 1999, 1998 and 1997
</TABLE>

            Schedules other than those listed above have been omitted since they
are either not required or the information is included elsewhere in the
financial statements or notes thereto.


                                       42
<PAGE>   3


             3.       List of Exhibits.

          2.01        Agreement and Plan of Merger, dated June 23, 1998 by and
                      between COMNET Corporation and Group 1 Software, Inc.
                      (incorporated by reference to the Company's Prospectus
                      filed August 18, 1998.)

          3.01        Articles of Incorporation and Bylaws, as amended - 1985,
                      (incorporated by reference to Exhibit 3.7 to Group 1's
                      Annual Report on Form 10-K for the year ended March 31,
                      1991).

          3.02        Bylaws - Amended as of January 22, 1992, (incorporated by
                      reference to Exhibit 3.8 to Group 1's Quarterly Report on
                      Form 10-Q for the quarter ended December 31, 1991).

          3.03        Amendments to Certificate of Incorporation filed January
                      22, 1993.

          4.01        Purchase Agreement between the Company and Medco
                      Containment Services, Inc., dated as of January 28, 1992
                      (incorporated by reference to Exhibit 4.47 to the
                      Company's Quarterly Report on Form 10-Q for the quarter
                      ended December 31, 1991).

          4.02        Agreement Regarding Satisfaction of Debt, Release of
                      Pledge and Issuance of Stock between Group 1 and Robert S.
                      Bowen, dated as of January 28, 1992, (incorporated by
                      reference to Exhibit 4.48 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.03        Agreement Regarding Satisfaction of Debt, Release of
                      Pledge and Issuance of Stock between Group 1 and Dr.
                      Milton Kaplan, dated as of January 28, 1992, (incorporated
                      by reference to Exhibit 4.49 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.04        Agreement Regarding Satisfaction of Debt, Release of
                      Pledge and Issuance of Stock between Group 1 and John
                      Spohler, dated as of January 28, 1992, (incorporated by
                      reference to Exhibit 4.50 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.05        Agreement Regarding Satisfaction of Debt, Release of
                      Pledge and Issuance of Stock between the Company and
                      Leonard J. Smith, dated as of January 28, 1992,
                      (incorporated by reference to Exhibit 4.51 to Group 1's
                      Quarterly Report on Form 10-Q for the quarter ended
                      December 31, 1991).

          4.06        Stock Option Agreement between the Company and James V.
                      Manning, dated as of August 16, 1991, (incorporated by
                      reference to Exhibit 4.53 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.07        Stock Option Agreement between the Company and James
                      Marden, dated as of August 16, 1991, (incorporated by
                      reference to Exhibit 4.55 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.08        Stock Option Agreement between the Company and Robert S.
                      Bowen, dated as of August 16, 1991, (incorporated by
                      reference to Exhibit 4.56 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.09        Stock Option Agreement between the Company and Ronald F.
                      Friedman, dated as of August 16, 1991, (incorporated by
                      reference to Exhibit 4.57 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

          4.10        Intentionally deleted


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<PAGE>   4

          4.11        Stock Option Agreement between the Company and Charles J.
                      Sindelar, dated as of August 16, 1991, (incorporated by
                      reference to Exhibit 4.59 to the Company's Quarterly
                      Report on From 10-Q for the quarter ended December 31,
                      1991).

          4.12        Agreement among the Company and Robert S. Bowen, Milton
                      Kaplan, Leonard J. Smith and John Spohler regarding
                      certain registration rights, dated as of January 28, 1992,
                      (incorporated by reference to Exhibit 4.60 to the
                      Company's Quarterly Report on Form 10-Q for the quarter
                      ended December 31, 1991).

          4.13        Certificate of Designation of 6% Convertible Preferred
                      Stock, filed January 22 1993.

          4.14        1995 Incentive Stock Option, Non-Qualified Stock Option
                      and Stock Appreciation Unit Plan

          4.15        1995 Non-Employee Directors' Stock Option Plan

         10.01        Intentionally deleted

         10.02        Intentionally deleted.

         10.03        Intentionally deleted

         10.04        Intentionally deleted.

         10.05        Tax Sharing Agreement among Group 1 Software, Inc.,
                      COM-MED Systems, Inc., ADMS, Inc. and COMNET Corporation,
                      dated April 1, 1991, (incorporated by reference to Exhibit
                      10.97 to the Company's Annual Report on Form 10-K for the
                      year March 31, 1991).

         10.06        First Amendment to Employment Agreement by and between
                      Group 1 Software, Inc. and Ronald F. Friedman dated June
                      24, 1991, (incorporated by reference to Exhibit 10.96 to
                      the Company's Quarterly Report on Form 10-Q for the
                      quarter ended June 3, 1991).

         10.07        Intentionally deleted

         10.08        Amended and Restated Employment Agreement dated January
                      28, 1992 by and between Group 1 Software, Inc. and Robert
                      S. Bowen (incorporated by reference to Exhibit 10.25 to
                      the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).

         10.09        Fee Agreement between the Company and James V. Manning,
                      dated as of January 28, 1992, (incorporated by reference
                      to Exhibit 10.100 to the Company's Quarterly Report on
                      Form 10-Q for the quarter ended December 31, 1991).

         10.10        Fee Agreement between the Company and Robert S. Bowen,
                      dated as of January 28, 1992, (incorporated by reference
                      to Exhibit 10.102 to the Company's Quarterly Report on
                      Form 10-Q for the quarter ended December 31, 1991).

         10.11        Fee Agreement between the Company and Ronald F. Friedman,
                      dated as of January 28, 1992, (incorporated by reference
                      to Exhibit 10.103 to the Company's Quarterly Report on
                      Form 10-Q for the quarter ended December 31, 1991).

         10.12        Indemnification Agreement between the Company and James
                      V. Manning, (incorporated by reference to Exhibit 10.105
                      to the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).


                                       44
<PAGE>   5

         10.13        Indemnification Agreement between the Company and James
                      P. Marden, (incorporated by reference to Exhibit 10.107
                      to the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).

         10.14        Indemnification Agreement between the Company and Ronald
                      F. Friedman , (incorporated by reference to Exhibit
                      10.108 to the Company's Quarterly Report on Form 10-Q for
                      the quarter ended December 31, 1991).

         10.15        Intentionally deleted

         10.16        Indemnification Agreement between the Company and Robert
                      S. Bowen, (incorporated by reference to Exhibit 10.110 to
                      the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).

         10.17        Stockholder Voting Agreement among Medco Containment
                      Services, Inc. and Robert S. Bowen, Charles A. Crew,
                      Ronald F. Friedman, Milton Kaplan, Perry E. Morrison,
                      Leonard J. Smith and John Spohler, dated as of January
                      28, 1992, (incorporated by reference to Exhibit 10.111 to
                      the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).

         10.18        Advisory Committee Agreement between the Company and
                      Leonard J. Smith, dated as of January 28, 1992,
                      (incorporated by reference to Exhibit 10.112 to the
                      Company's Quarterly Report on Form 10-Q for the quarter
                      ended December 31, 1991).

         10.19        Advisory Committee Agreement between the Company and
                      Milton Kaplan, dated as of January 28, 1992, (incorporated
                      by reference to Exhibit 10.113 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

         10.20        Advisory Committee Agreement between the Company and Perry
                      E. Morrison, dated as of January 28, 1992, (incorporated
                      by reference to Exhibit 10.114 to the Company's Quarterly
                      Report on Form 10-Q for the quarter ended December 31,
                      1991).

         10.21        Agreement between the Company and Robert S. Bowen, dated
                      as of January 23, 1992, (incorporated by reference to
                      Exhibit 10.115 to the Company's Quarterly Report on Form
                      10-Q for the quarter ended December 31, 1991).

         10.22        Intentionally deleted

         10.23        Amended and Restated Employment Agreement between Robert
                      S. Bowen and the Company, dated as of January 28, 1992,
                      (incorporated by reference to Exhibit 10.118 to the
                      Company's Quarterly Report on Form 10-Q for the quarter
                      ended December 31, 1991).

         10.24        Amended and Restated Employment Agreement between Robert
                      S. Bowen and Group 1 Software, Inc., dated as of January
                      28, 1992, (incorporated by reference to Exhibit 10.119 to
                      the Company's Quarterly Report on Form 10-Q for the
                      quarter ended December 31, 1991).

         10.25        Intentionally deleted

         10.26        Loan Agreement, dated March 1, 1993, between COMNET
                      Corporation and Ronald F. Friedman.

         10.27        Indemnification Agreement, dated February 24, 1992,
                      between COMNET Corporation and Charles A. Mele.

         10.28        Indemnification Agreement between COMNET Corporation and
                      Charles J. Sindelar.

         10.29        Lease covering Company office facilities in Lanham, MD -
                      1993.

         10.30        Intentionally deleted.


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<PAGE>   6

         10.31        Intentionally deleted

         10.32        Fourth Amendment to Employment Agreement, dated as of
                      March 1, 1994, by and between Group 1 Software, Inc., and
                      Ronald F. Friedman.

         10.33        Intentionally deleted

         10.34        Intentionally deleted

         10.35        Intentionally deleted.

         10.36        Intentionally deleted

         10.37        Intentionally deleted

         10.38        Intentionally deleted

         10.39        Intentionally deleted

         10.40        Fifth Amendment to Employment Agreement, dated as of
                      April 1, 1995, by and between Group 1 Software, Inc. and
                      Ronald F. Friedman.

         10.41        COMNET Corporation, Deferred Compensation Plan

         10.42        Definitive Agreement for purchase of assets of
                      DataDesigns, Inc., dated August 23, 1995 (incorporated by
                      reference to Exhibit 10.42 to the Company's Annual Report
                      on Form 10-K for the year ended March 31, 1997).

         10.43        Intentionally deleted

         10.44        Agreement between Sidco, Inc., and CMEDS, Inc., dated
                      November 14, 1995 (incorporated by reference to Exhibit
                      10.44 to the Company's Annual Report on Form 10-K for the
                      year ended March 31, 1997).

         10.45        Third Amendment to Lease, dated April 15, 1994, by and
                      between COMNET Corporation and Quadrangle Development
                      Corporation (incorporated by reference to Exhibit 10.45 to
                      the Company's Annual Report on Form 10-K for the year
                      ended March 31, 1997).

         10.46        First Amendment to Sublease, dated April 15, 1994, by and
                      between COMNET Corporation and Group 1 Software, Inc.
                      (incorporated by reference to Exhibit 10.46 to the
                      Company's Annual Report on Form 10-K for the year ended
                      March 31, 1997).

         10.47        First Amendment to Loan Agreement with Ronald F.
                      Friedman, dated as of January 15, 1996.

         10.48        Line of Credit Loan Agreement with Crestar Bank, dated
                      October 10, 1996.

         10.49        Agreement to Extend Management and Services Agreement,
                      dated April 1, 1997, by and between the Company and Group
                      1 Software, Inc.

         10.50        First Amendment to Employment Agreement by and between
                      Robert S. Bowen and COMNET Corporation, dated August 15,
                      1997.

         10.51        Second Amendment to Employment Agreement by and between
                      Robert S. Bowen and COMNET


                                       46
<PAGE>   7
                      Corporation, dated January 12, 1998.

         10.52        Third Amendment to Employment Agreement by and between
                      Robert S. Bowen and Group 1 Software, Inc. dated August
                      15, 1997.

         10.53        Fourth Amendment to Employment Agreement by and between
                      Robert S. Bowen and Group 1 Software, Inc. dated January
                      12, 1998.

         10.54        Fifth Amendment to Employment Agreement by and between
                      Robert S. Bowen and Group 1 Software, Inc. dated May 11,
                      1998.

         10.55        Agreement for Purchase and Sale of Assets by and between
                      Intertrak Corporation and Group 1 Software, Inc. dated
                      September 4, 1997.

        *10.56        Agreement to repurchase preferred and common stock from
                      Merck & Co Inc. dated September 25, 1998.

         *22.0        Subsidiaries of Group 1 Software, Inc.

         *23.1        Consent of PricewaterhouseCoopers LLP.

         *27.0        Financial Data Schedule

-------------------------------
         *  Filed herewith.


                                       47
<PAGE>   8

                        REPORT OF INDEPENDENT ACCOUNTANTS
                         ON FINANCIAL STATEMENT SCHEDULE

                                -----------------

To the Board of Directors of
 Group 1 Software, Inc.

       Our audits of the consolidated financial statements referred to in our
reports dated June 4, 1999 appearing in the 1999 Annual Report to Shareholders
of Group 1 Software, Inc. (which report and consolidated financial statements
are included in this Annual Report on Form 10-K) also included an audit of the
financial statement schedule listed in Item 14(2) of this Annual Report on Form
10-K. In our opinion, this financial statement schedule presents fairly, in all
material respects, the information set forth therein when read in conjunction
with the related consolidated financial statements.

PricewaterhouseCoopers LLP

McLean, Virginia
June 4, 1999


                                       48
<PAGE>   9


                                  SCHEDULE II
                             GROUP 1 SOFTWARE, INC.
VALUATION AND QUALIFYING ACCOUNTS FOR THE YEARS ENDED MARCH 31, 1999, 1998,
                                    AND 1997
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
           Column A               Column B         Column C      Additions        Column D         Column E
--------------------------   ------------------  ---------------------------  ---------------  -------------
                                Balance at        Charged to     Charged to                       Balance
                                 Beginning         Costs and       Other         Deductions       at end
           Description            of Year          Expenses       Accounts       Describe(1)      of year
           -----------          ----------        ----------     ----------     ------------    ------------
<S>                           <C>                <C>            <C>            <C>              <C>
Year ended March 31, 1999      $  3,603           $  2,955        - - -          $ (3,175)       $   3,383
  Allowance for  doubtful
  accounts

Year ended March 31, 1998
  Allowance for  doubtful      $  3,208           $  3,505        - - -          $ (3,110)       $   3,603
  accounts

Year ended March 31, 1997
  Allowance for  doubtful      $  2,409           $  1,956        - - -          $ (1,157)       $   3,208
  accounts
</TABLE>

-----------------------------

(1)    The decrease in allowance for doubtful accounts is the result of accounts
       receivable written off during the year.


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<PAGE>   10

                                   SIGNATURES

       Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized.

  GROUP 1 SOFTWARE, INC.

                                     (Registrant)

Date:  June 29, 1999                       By:
                                              ---------------------------------
                                                     Chief Executive Officer

       Pursuant to the requirements of the Securities Exchange Act of 1934, this
Report has been signed below by the following persons on behalf of the
Registrant and in the capacities and on the dates indicated.

<TABLE>
<CAPTION>
Signature                          Title                                        Date
---------                          ------                                       ----
<S>                               <C>                                          <C>


------------------------------
Robert S. Bowen                    Chief Executive                              June 29, 1999
                                   Officer and Director                         -------------
                                   (Principal Executive Officer)

------------------------------
Mark D. Funston                    Vice President                               June 29, 1999
                                   Chief Financial Officer                      -------------
                                   Treasurer (Principal Financial and
                                   Accounting Officer)

------------------------------
Ronald F. Friedman                 President and Director                       June 29, 1999
                                                                                -------------

------------------------------
James V. Manning                   Chairman of the Board                        June 29, 1999
                                                                                -------------

------------------------------
Charles J. Sindelar                Director                                     June 29, 1999
                                                                                -------------

------------------------------
James Marden                       Director                                     June 29, 1999
                                                                                -------------

------------------------------
Charles A. Mele                    Director                                     June 29, 1999
                                                                                -------------

------------------------------
Richard H. Eisenberg               Director                                     June 29, 1999
                                                                                -------------

------------------------------
Bruce J. Spohler                   Director                                     June 26, 1999
                                                                                -------------

------------------------------
Thomas S. Buchsbaum                Director                                     June 29, 1999
                                                                                -------------
</TABLE>


                                       50
<PAGE>   11

Index of Exhibits



         *10.56       Agreement to repurchase preferred and
                      common stock from Merck & Co Inc. dated
                      September 25, 1998.

         *22.0        Subsidiaries of Group 1 Software, Inc.

         *23.1        Consent of PricewaterhouseCoopers, LLP

         *27.0        Financial Data Schedule

-------------------------------
         *  Filed herewith.


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